I actually found the code here: http://code.open-bio.org/svnweb/index.cgi/biojava/view/biojava-live/trunk/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/TreesBlock.java
But I absolutely have now idea if it was distributed or packaged for the general public. Clearly the API docs do not have that version. Tiago (not a biojava developer, just someone who heavily patched the nexus parser long time ago) 2010/11/1 filip <[email protected]>: > On Mon, 1 Nov 2010 17:39:03 +0000 > Tiago Antão <[email protected]> wrote: > >> Hi, >> >> Biojava does have org.biojavax.bio.phylo.io.nexus. Sometime ago I >> refactored that code and made an example with it: >> http://tiago.org/cc/2009/11/17/reading-newicknexus-phylogenetic-trees-with-biojava/ >> I don't know if this suites you needs. >> If you find a bug with the code, just drop an email here on the list >> and I will take care of it (time permitting). >> >> On Mon, Nov 1, 2010 at 4:20 PM, filip <[email protected]> wrote: >> > Hi, >> > I would like to write a class with methods for parsing tip labels, >> > edges (parent-sibling) and edge lengths from nexus tree file (single >> > tree block). Could You point me to some biojava classes I could use? >> > >> > _______________________________________________ >> > Biojava-l mailing list - [email protected] >> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> > >> >> >> > > > Hi, > > Thank You for the swift response - I tried the code snippets from > Tiago's blog. It seems that the version of API I posess does not > have "getTopNode()" method for TreesBlock class: > > TreesBlock node = getTreeNode(nexus); > WeightedGraph<String, DefaultWeightedEdge> graph = > node.getTreeAsWeightedJGraphT(name); topNode = > node.getTopNode(); > > My quick search through the sources confirms that. > > I will also take a look at forester libs - thank You for the tip. Are > there any code examples for those I can look at? > > > -- > while(!succeed) { try(); } > -- "If you want to get laid, go to college. If you want an education, go to the library." - Frank Zappa _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
